7PLR
Crystal structure of the N-terminal endonuclease domain of La Crosse virus L-protein bound to compound Baloxavir
X-RAY DIFFRACTION
Starting Model(s)
Initial Refinement Model(s) | |||
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Type | Source | Accession Code | Details |
experimental model | PDB | 7OA4 |
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, SITTING DROP | 8 | 293 | 3.4M Sodium Formate 0.1M Tris - HCl pH8.0 |
Crystal Properties | |
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Matthews coefficient | Solvent content |
3.82 | 67.76 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 124.738 | ¦Á = 90 |
b = 124.738 | ¦Â = 90 |
c = 295.25 | ¦Ã = 120 |
Symmetry | |
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Space Group | P 61 2 2 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 100 | PIXEL | DECTRIS EIGER X 16M | 2020-07-23 | M | SINGLE WAVELENGTH |
Radiation Source | |||||
---|---|---|---|---|---|
ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 | SYNCHROTRON | SOLEIL BEAMLINE PROXIMA 1 | 0.97856 | SOLEIL | PROXIMA 1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | |||||||
1 | 2.64 | 108.03 | 100 | 0.025 | 0.999 | 20.1 | 39.8 | 40890 |
Highest Resolution Shell | |||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | Rpim I (All) | CC (Half) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | ||||||||||
1 | 2.64 | 2.69 | 100 | 0.19 | 0.912 | 2.2 | 39.1 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (All) | R-Work | R-Free | Mean Isotropic B | |||||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | FREE R-VALUE | 7OA4 | 2.64 | 108.026 | 40799 | 2041 | 100 | 0.216 | 0.2136 | 0.2539 | 55.557 |
Temperature Factor Modeling | ||||||
---|---|---|---|---|---|---|
Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.811 | 0.406 | 0.811 | -2.632 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
r_dihedral_angle_2_deg | 33.307 |
r_dihedral_angle_3_deg | 14.438 |
r_dihedral_angle_4_deg | 12.758 |
r_dihedral_angle_1_deg | 5.503 |
r_lrange_it | 4.608 |
r_lrange_other | 4.598 |
r_scangle_it | 2.853 |
r_scangle_other | 2.853 |
r_mcangle_it | 2.687 |
r_mcangle_other | 2.686 |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 6132 |
Nucleic Acid Atoms | |
Solvent Atoms | 63 |
Heterogen Atoms | 130 |
Software
Software | |
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Software Name | Purpose |
REFMAC | refinement |
xia2 | data reduction |
DIALS | data scaling |
PHASER | phasing |